Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

2017-04-04 Thread Maarten van Iterson 
Thanks for looking into this!

Maarten

On Mon, Apr 3, 2017 at 7:00 PM, Hervé Pagès  wrote:

> Hi Maarten,
>
> identical() is not reliable on DNAStringSet objects or other objects
> that contain external pointers as it can return false negatives as well
> as false positives. We'll fix the "cbind" and "rbind" methods for
> SummarizedExperiment to work around this problem.
>
> Thanks for the report.
>
> H.
>
>
> On 04/03/2017 12:58 AM, Maarten van Iterson wrote:
>
>> Dear list,
>>
>> Combining SummarizedExperiment object, containing a DNAStringSet in the
>> rowData seems not to work properly. If I cbind two SummarizedExperiment
>> objects, which I know are identical, an error is reported:
>>
>> Error in FUN(X[[i]], ...) (from #2) :
>>   column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not
>> match
>>
>> I think I traced the problem existing in `SummarizedExperiment:::.compa
>> re`
>> in that `identical` is used to compare DNAStringSets which is not behaving
>> as expected. Whereas it should return all identical it returns it is not!
>>
>> Here is a counter example (which was easier to construct) showing that
>> `identical` returns FALSE where it should return TRUE.
>>
>> library(Biostrings)
>>> seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>>> seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>>>
>>> seq1
>>>
>> [1] "GACTC"
>>
>>> seq2
>>>
>> [1] "GAATG"
>>
>>>
>>> s1 <- DNAStringSet(seq1)
>>> s2 <- DNAStringSet(seq2)
>>>
>>> str(s1)
>>>
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
>> with 2 slots
>>   .. .. ..@ xp_list:List of 1
>>   .. .. .. ..$ :
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :
>>   ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
>> with 7 slots
>>   .. .. ..@ group  : int 1
>>   .. .. ..@ start  : int 1
>>   .. .. ..@ width  : int 5
>>   .. .. ..@ NAMES  : NULL
>>   .. .. ..@ elementType: chr "integer"
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ metadata   : list()
>>   ..@ elementType: chr "DNAString"
>>   ..@ elementMetadata: NULL
>>   ..@ metadata   : list()
>>
>>> str(s2)
>>>
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
>> with 2 slots
>>   .. .. ..@ xp_list:List of 1
>>   .. .. .. ..$ :
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :
>>
>>   ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
>> with 7 slots
>>   .. .. ..@ group  : int 1
>>   .. .. ..@ start  : int 1
>>   .. .. ..@ width  : int 5
>>   .. .. ..@ NAMES  : NULL
>>   .. .. ..@ elementType: chr "integer"
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ metadata   : list()
>>   ..@ elementType: chr "DNAString"
>>   ..@ elementMetadata: NULL
>>   ..@ metadata   : list()
>>
>>>
>>> identical(seq1, seq2)
>>>
>> [1] FALSE
>>
>>> identical(s1, s2)
>>>
>> [1] TRUE
>>
>>> seq1 == seq2
>>>
>> [1] FALSE
>>
>>> s1 == s2
>>>
>> [1] FALSE
>>
>>>
>>> sessionInfo()
>>>
>> R version 3.3.2 (2016-10-31)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.2 LTS
>>
>> locale:
>>  [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
>>  [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
>>  [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
>>  [7] LC_PAPER=en_US.utf8   LC_NAME=C
>>  [9] LC_ADDRESS=C  LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats4stats graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] Biostrings_2.42.1  XVector_0.14.1
>>  [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4.0
>>  [5] Biobase_2.34.0 GenomicRanges_1.26.4
>>  [7] GenomeInfoDb_1.10.3IRanges_2.8.2
>>  [9] S4Vectors_0.12.2   BiocGenerics_0.20.0
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.10 AnnotationDbi_1.36.2
>> hms_0.3
>>  [4] GenomicAlignments_1.10.1 zlibbioc_1.20.0
>> BiocParallel_1.8.1
>>  [7] BSgenome_1.42.0  lattice_0.20-35
>> R6_2.2.0
>> [10] httr_1.2.1   tools_3.3.2
>> grid_3.3.2
>> [13] DBI_0.6  assertthat_0.1
>> digest_0.6.12
>> [16] tibble_1.2   Matrix_1.2-8
>> readr_1.1.0
>> [19] rtracklayer_1.34.2   bitops_1.0-6
>> biomaRt_2.30.0
>> [22] RCurl_1.95-4.8   memoise_1.0.0
>> RSQLite_1.1-2
>> [25] compiler_3.3.2   GenomicFeatures_1.26.3
>> Rsamtools_1.26.1
>> [28] XML_3.98-1.5 jsonlite_1.3
>> VariantAnnotation_1.20.3
>>
>>>
>>>
>> I don't completely understand understand why `identical` is not working
>> properly is it comparing the environment address

Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

2017-04-03 Thread Hervé Pagès 

Hi Maarten,

identical() is not reliable on DNAStringSet objects or other objects
that contain external pointers as it can return false negatives as well
as false positives. We'll fix the "cbind" and "rbind" methods for
SummarizedExperiment to work around this problem.

Thanks for the report.

H.

On 04/03/2017 12:58 AM, Maarten van Iterson wrote:

Dear list,

Combining SummarizedExperiment object, containing a DNAStringSet in the
rowData seems not to work properly. If I cbind two SummarizedExperiment
objects, which I know are identical, an error is reported:

Error in FUN(X[[i]], ...) (from #2) :
  column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not match

I think I traced the problem existing in `SummarizedExperiment:::.compare`
in that `identical` is used to compare DNAStringSets which is not behaving
as expected. Whereas it should return all identical it returns it is not!

Here is a counter example (which was easier to construct) showing that
`identical` returns FALSE where it should return TRUE.


library(Biostrings)
seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")

seq1

[1] "GACTC"

seq2

[1] "GAATG"


s1 <- DNAStringSet(seq1)
s2 <- DNAStringSet(seq2)

str(s1)

Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :
  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()

str(s2)

Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :

  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()


identical(seq1, seq2)

[1] FALSE

identical(s1, s2)

[1] TRUE

seq1 == seq2

[1] FALSE

s1 == s2

[1] FALSE


sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8   LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] Biostrings_2.42.1  XVector_0.14.1
 [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4.0
 [5] Biobase_2.34.0 GenomicRanges_1.26.4
 [7] GenomeInfoDb_1.10.3IRanges_2.8.2
 [9] S4Vectors_0.12.2   BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10 AnnotationDbi_1.36.2
hms_0.3
 [4] GenomicAlignments_1.10.1 zlibbioc_1.20.0
BiocParallel_1.8.1
 [7] BSgenome_1.42.0  lattice_0.20-35
R6_2.2.0
[10] httr_1.2.1   tools_3.3.2
grid_3.3.2
[13] DBI_0.6  assertthat_0.1
digest_0.6.12
[16] tibble_1.2   Matrix_1.2-8
readr_1.1.0
[19] rtracklayer_1.34.2   bitops_1.0-6
biomaRt_2.30.0
[22] RCurl_1.95-4.8   memoise_1.0.0
RSQLite_1.1-2
[25] compiler_3.3.2   GenomicFeatures_1.26.3
Rsamtools_1.26.1
[28] XML_3.98-1.5 jsonlite_1.3
VariantAnnotation_1.20.3




I don't completely understand understand why `identical` is not working
properly is it comparing the environment address in the above example they
are the same although the sequences are not? In my case the two
SummarizedExperiments contained the same DNAStringSets but had a different
environment address?

Regards,
Maarten

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